Tag: kegg

KEGG T30512: 29135     T30512 (Metagenome): 29135 Help Entry 29135             CDS       T30512                                  Symbol fbp Name fructose-1,6-bisphosphatase class 1   KO Best hit Taxonomy Gammaproteobacteria – Others [GN:hin]Taxonomy Pathway 00010   Glycolysis / Gluconeogenesis 00030   Pentose phosphate pathway 00051   Fructose and mannose metabolism 00680   Methane metabolism 00710   Carbon fixation in photosynthetic organisms 01100   Metabolic pathways…

KEGG T30512: 12494     T30512 (Metagenome): 12494 Help Entry 12494             CDS       T30512                                  Name pyruvate dehydrogenase subunit E1   KO Best hit Taxonomy Actinobacteria [GN:acq]Taxonomy Pathway 00010   Glycolysis / Gluconeogenesis 00020   Citrate cycle (TCA cycle) 00620   Pyruvate metabolism 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 01120   Microbial metabolism in diverse environments 01200   Carbon…

Entry 118725205         ncRNA     T07682                                  Name (RefSeq) U1 spliceosomal RNA   KO K14276   U1 spliceosomal RNA Organism pkl  Pipistrellus kuhlii (Kuhl’s pipistrelle) Pathway pkl03040   Spliceosome Brite KEGG Orthology (KO) [BR:pkl00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    118725205 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03041 Spliceosome [BR:pkl03041]    118725205  09184 RNA family   03100 Non-coding RNAs [BR:pkl03100]    118725205Spliceosome [BR:pkl03041] Splicing related RNAs  118725205Non-coding RNAs [BR:pkl03100] Small non-coding…

Entry 4332822           CDS       T01015                                  Name (RefSeq) LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like   KO K12882   nuclear cap-binding protein subunit 1 Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa03013   Nucleocytoplasmic transport osa03015   mRNA surveillance pathway osa03040   Spliceosome Brite KEGG Orthology (KO) [BR:osa00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    4332822  09122 Translation   03013 Nucleocytoplasmic transport    4332822   03015 mRNA…

KEGG ORTHOLOGY: K06121     ORTHOLOGY: K06121 Help Entry K06121                      KO                                      Symbol dhbC Name glycerol dehydratase medium subunit [EC:4.2.1.30] Pathway Reaction R01047   glycerol hydro-lyase (3-hydroxypropanal-forming) Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism  09103 Lipid metabolism   00561 Glycerolipid metabolism    K06121  dhbC; glycerol dehydratase medium subunitEnzymes [BR:ko01000] 4. Lyases  4.2  Carbon-oxygen lyases   4.2.1  Hydro-lyases    4.2.1.30  glycerol dehydratase     K06121  dhbC; glycerol dehydratase medium subunit BRITE hierarchy Other DBs Genes…

Entry 100782702         CDS       T01710                                  Symbol COX2 Name (RefSeq) cytochrome c oxidase subunit 2, mitochondrial   KO K02261   cytochrome c oxidase subunit 2 Organism gmx  Glycine max (soybean) Pathway gmx00190   Oxidative phosphorylation gmx01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:gmx00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    100782702 (COX2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03029 Mitochondrial biogenesis…

Single nucleus RNA-seq reveals cell type heterogeneity in human SNpc We sampled SNpc from post-mortem human brains of 15 sporadic Parkinson’s disease (PD) patients and 14 Control individuals (see Supplementary Table 1 for full pathology reports). Using a 10X Genomics Chromium platform, we performed single nucleus RNA-seq (snRNA-seq) on more than…

Capturing proteins associated with SARS-CoV-2 virions To identify host cell proteins potentially present in extracellular SARS-CoV-2 virions, viral particles were produced from two lung epithelial cell models, A549 cells overexpressing ACE2 receptor (A549-ACE2) and Calu-3 cells that naturally express ACE2 receptor and TMPRSS2. Following infection with the D614G SARS-CoV-2 strain32,…

Entry IA203_01755       CDS       T08053                                  Name (GenBank) UDP-N-acetylmuramate dehydrogenase   KO K00075   UDP-N-acetylmuramate dehydrogenase [EC:1.3.1.98] Organism cwk  Corynebacterium wankanglinii Pathway cwk00520   Amino sugar and nucleotide sugar metabolism cwk00550   Peptidoglycan biosynthesis cwk01100   Metabolic pathways cwk01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:cwk00001] 09100 Metabolism  09101 Carbohydrate metabolism   00520 Amino sugar and nucleotide sugar metabolism    IA203_01755  09107 Glycan biosynthesis and…

Entry BWI76_09435       CDS       T09148                                  Name (GenBank) glutaredoxin, GrxA family   KO K03674   glutaredoxin 1 Organism klm  Klebsiella sp. M5al Brite KEGG Orthology (KO) [BR:klm00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03110 Chaperones and folding catalysts [BR:klm03110]    BWI76_09435Chaperones and folding catalysts [BR:klm03110] Protein folding catalysts  Protein disulfide isomerase   BWI76_09435 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam:  Glutaredoxin Glrx-like Thioredoxin_3…

Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…

Genome assembly and annotation The DNA sequencing data (1119.58 Gb, average 110× coverage) of the A. konjac sample were obtained using the Illumina Hiseq 2500 sequencer. A summary of the sequence data used for the assembly is presented in Table S1. The estimated genome size is 4,512,012,462 bp using 19-mer frequency distribution based…

Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…

Details Posted: 19-Dec-23 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Chicago, IL Job Description: Development of an integrated data warehouse for symbiote including clinical, microbiome sequence, and metabolomic data.  Management of DFI Biobank, MMF, and HMMF data within the Symbiote platform. Functional analysis of…

Department BSD DFI – Translational Informatics About the Department The Duchossois Family Institute focuses on the role of commensal bacteria in enhancing disease resistance and is using genomic and metabolomic platforms to characterize the microbiome and its metabolites. Computational and bioinformatic expertise is required to understand how commensal bacteria impact…

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

How to obtain the gene set of KEGG module 0 KEGG curatelly collect the pathway information including biological process and disease development. Each pathway has genes involved in pathway activity. The pathway has several modules with different function. Therefore, How to obtain the gene set of KEGG module R set…

Background: Catheter-based pulmonary vein isolation (PVI) is an effective and well-established intervention for symptomatic paroxysmal atrial fibrillation (PAF). Nevertheless, late recurrences of atrial fibrillation (LRAF) occurring during 3 to 12 months are common, and the underlying mechanisms remain elusive. Circular RNAs (circRNAs) in atrial tissue have been linked to the…

Diversity and compositional analyses Regarding clinical differences (Table 1), T2DM individuals (mean 69.6 (± 12.3 sd) years) were significantly (p value < 0.01; Wilcoxon rank-sum test) older than the controls (46.9 (± 17.3 sd) years), showed higher BMI (mean 30.9 (± 7.01 sd) vs. mean 26.3 (± 6.12 sd) than the control…

Enrichment dotplot color 0 Hi, I have a question about enrichGO or enrichKEGG dotplot. The dotplot I drew when using enrichGO() or enrichKEGG() was this color: But when I repainted it today it turned into this color: And I can’t change it back, can anyone help me get it back…

Introduction Skin cutaneous melanoma (SKCM), as one of the most aggressive types of cancer due to its elevated degree of heterogeneity, has gained increasing attention during the past few decades.1 Also known as “the cancer that rises with the sun”,2 melanoma originates from cancerous melanocytes due to molecular or genetic…

DOI: 10.18129/B9.bioc.clusterProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…

Dynamic mRNA signatures in the early phase of epileptogenesis after Pilocarpine-induced SE To decipher transcriptional changes early after pilocarpine-induced SE in the hippocampal CA1 subfield, we compared mRNA expression profiles of pilocarpine-induced SE animals and non-SE controls in hippocampal CA1 at five different time points, i.e. 6, 12, 24, 36…

Whole genome sequencing and analysis To understand the mechanisms underlying the biological control capability of bacterial pathogens, the complete genome of MEP218 was sequenced, assembled, and deposited in the GenBank database under the accession number CP042864.2. The genome of MEP218 consists of a single circular chromosome of 3,944,892 bp with a…

Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…

Database for immunological pathways 0 Hello all, I was wondering if anyone knows of any databases that host pathways that are specific to human immunology. Ideally, I am looking for a table format data with each row containing a single immunological process and the genes that are participating in the…

Website or tool to obtain a list of genes that participate in a specific process? 1 Hello Biostar community, I hope you’re all doing well. I’m currently conducting research where we’ve observed cell death following treatment with a specific drug. However, we’re still in the dark about the underlying mechanism,…

mTORC1 signaling in bladder cancer Initially, we assessed the mTORC1 signaling scores of both normal and bladder cancer samples. We analyzed the TCGA dataset and observed that the mTORC1 signaling score in normal tissues was considerably lower than that in breast cancer tissue samples (Fig. 2A). We analyzed the expression of…

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

CHEK2 expression increased in cancer tissues First, the expression levels of CHEK2 in different tumor types in the TIMER database were evaluated. All tumors except for chromophobe renal cell carcinoma (KICH) showed elevated levels of CHEK2 expression compared to normal cells (Fig. 1A). Similarly, CHEK2 protein expression was upregulated in all…

Selection of 152 ALI-related genes (ALIRGs) by weighted gene co-expression network analysis (WGCNA) The samples of the GSE16409, GSE18341 and GSE102016 datasets were discretely distributed before merging, and the sample data (ALI = 21 and control = 14) was uniform after batch processing (Supplementary Fig. 1a,b). To identify the ALIRGs, the WGCNA was performed in…

KEGG T30512: 26705     T30512 (Metagenome): 26705 Help Entry 26705             CDS       T30512                                  Name   KO Best hit Taxonomy Actinobacteria [GN:acq]Taxonomy Pathway 00230   Purine metabolism 01100   Metabolic pathways 05340   Primary immunodeficiency Other DBs LinkDB All DBs Position C1167575:complement(3..554) AA seq 184 aa AA seqDB searchRLAVRYAGDQPGEVIGFGLSNDERAGQTSSWERAFAIARRGGLASMPHGGELLGPDHLREVVSCLGPTRLGHGVRAGEDPALLDAIVASGISLEVCPASNVSLGVYHSPDDVPLRRLMSHGAQIALSADDPLLFQSRLVDQYEIARTLGCDDAELAELARGSIRACLASPTAKQTWLAEVDAWL     T30512 (Metagenome): 26591 Help Entry 26591             CDS       T30512                                  Name   KO…

KEGG T30376: 31478     T30376 (Metagenome): 31478 Help Entry 31478             CDS       T30376                                  Name succinate dehydrogenase subunit A   KO Best hit Taxonomy Bacteroidetes [GN:afd]Taxonomy Pathway 00020   Citrate cycle (TCA cycle) 00190   Oxidative phosphorylation 00650   Butanoate metabolism 00720   Carbon fixation pathways in prokaryotes 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 01120   Microbial metabolism…

KEGG T30201: 12043     T30201 (Metagenome): 12043 Help Entry 12043             CDS       T30201                                  Name probable aspartate aminotransferase   KO K00816   kynurenine—oxoglutarate transaminase / cysteine-S-conjugate beta-lyase / glutamine—phenylpyruvate transaminase [EC:2.6.1.7 4.4.1.13 2.6.1.64] Best hit Pathway 00270   Cysteine and methionine metabolism 00380   Tryptophan metabolism 00450   Selenocompound metabolism 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 05204  …

KEGG T30641: 73770     T30641 (Metagenome): 73770 Help Entry 73770             CDS       T30641                                  Symbol glk Name   KO Best hit Pathway 00010   Glycolysis / Gluconeogenesis 00052   Galactose metabolism 00500   Starch and sucrose metabolism 00520   Amino sugar and nucleotide sugar metabolism 00521   Streptomycin biosynthesis 00524   Neomycin, kanamycin and gentamicin biosynthesis 01100   Metabolic pathways 01110   Biosynthesis…

ISCA fabrication VeroGray polymer was used to create 3D-printed moulds on an Objet30 3D printer (Stratasys), using previously described protocols32. Each ISCA consisted of 25 wells arranged in a 5 × 5 array. Each 110 µL well possessed a 800-μm-diameter port that connected the inside of the well with the surrounding seawater and…

Clinical features of WMI and nWMI groups From April 2022 to December 2022, the Affiliated Hospital of Guangdong Medical University enrolled a total of 83 subjects who met the inclusion criteria. The study finally included 71 cases after excluding 4 deaths, 6 patients who failed to complete MRI + DTI testing, 1…

Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…

Kaiyuan Zhang,1,&ast; Ziyue Luo,1,&ast; Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…

Yang J, Liu X, Cao S, Dong X, Rao S, Cai K. Understanding esophageal cancer: the challenges and opportunities for the next decade. Front Oncol. 2020;10:1727. Article  PubMed  PubMed Central  Google Scholar  Li J, Xu J, Zheng Y, Gao Y, He S, Li H, et al. Esophageal cancer: epidemiology, risk…

KEGG ENZYME: 2.4.1.295     ENZYME: 2.4.1.295 Help Entry EC 2.4.1.295                Enzyme                                  Name anthocyanin 3-O-sambubioside 5-O-glucosyltransferase Class Transferases;Glycosyltransferases;HexosyltransferasesBRITE hierarchy Sysname UDP-alpha-D-glucose:anthocyanidin-3-O-beta-D-sambubioside 5-O-glucosyltransferase Reaction(IUBMB) UDP-alpha-D-glucose + an anthocyanidin 3-O-beta-D-sambubioside = UDP + an anthocyanidin 5-O-beta-D-glucoside 3-O-beta-D-sambubioside [RN:R10265] Reaction(KEGG) Substrate UDP-alpha-D-glucose [CPD:C00029]; anthocyanidin 3-O-beta-D-sambubioside [CPD:C20467] Product UDP [CPD:C00015]; anthocyanidin 5-O-beta-D-glucoside 3-O-beta-D-sambubioside [CPD:C20474] Comment Isolated from…

extracting Uniprot IDs for Kegg pathways 0 I would like to know if it is possible to extract the UniProt IDs for each of the KEGG pathways for specific organisms. From reading the clusterProfiler documentation, I think the information is all there, I’m just not sure, how one can access…

Introduction Leprosy is a disabling infectious disease that predominantly occurs in the skin and peripheral nerves and is transmitted by contact with pathogenic bacteria through the respiratory tract and broken skin. Leprosy is attributed to infection with Mycobacterium leprae (M. leprae)1 and the more recently discovered Mycobacterium lepromatosis.2 In addition,…

KEGG REACTION: R05959     REACTION: R05959 Help Entry R05959                      Reaction                                Definition CMP-N-acetylneuraminate + GM1b <=> CMP + GD1a Equation Comment Siat7c, Siat7d, Siat7e, Siat7f Enzyme Pathway rn00604   Glycosphingolipid biosynthesis – ganglio series Brite Enzymatic reactions [BR:br08201] 2. Transferase reactions  2.4  Glycosyltransferases   2.4.3  Sialyltransferases    2.4.3.7     R05959  CMP-N-acetylneuraminate + GM1b <=> CMP + GD1aIUBMB reaction hierarchy [BR:br08202] 2. Transferase reactions  2.4.3.7   R04635  alpha-N-Acetylneuraminyl-2,3-beta-D-galactosyl-1,3-N-acetyl-D-galactosaminyl-R <=> alpha-N-Acetylneuraminyl-2,3-beta-D-galactose-1,3-(alpha-N-acetylneuraminyl-2,6)-N-acetyl-D-galactosaminyl-R    R05959  GM1b…

KEGG REACTION: R07728     REACTION: R07728 Help Entry R07728                      Reaction                                Name (6aR,11aR)-3,9-dihydroxypterocarpan:NADP+ 2′-oxidoreductase Definition 2′-Hydroxydihydrodaidzein + NADPH + H+ <=> 3,9-Dihydroxypterocarpan + NADP+ + H2O Equation Reaction class Pathway rn00943   Isoflavonoid biosynthesis rn01110   Biosynthesis of secondary metabolites LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

Effects of DA on potential N transformation rates It was reported that DIN in overlying water is mainly from sediments25, so the variation of DIN concentrations in overlying water was monitored, so as to infer the potential N transformation process in sediments. Generally, it can be observed that the overlying…

Entry 9853              CDS       T30943                                  Symbol 85_SUR_0d2-3_scaffold13655_1_gene9853 Name strand:- start:118 stop:714 length:597 start_codon:no stop_codon:yesgene_type:incomplete   KO K00939   adenylate kinase [EC:2.7.4.3] Best hit pub:SAR11_1096 (best score: 334.724) Taxonomy Alphaproteobacteria [GN:pub]Taxonomy Pathway 00230   Purine metabolism 00730   Thiamine metabolism 01100   Metabolic pathways 01110   Biosynthesis of secondary metabolites 01240   Biosynthesis of cofactors LinkDB All DBs AA seq 198…

Identification of the SKCM necroptosis cluster The comprehensive analysis encompassed a total of 803 patients drawn from five distinct melanoma cohorts, namely, TCGA-SKCM, GSE65094, GSE53118, GSE54467, and GSE19234. Employing an unsupervised clustering algorithm, we stratified melanoma patients based on their NRG expression profiles. This facilitated a deeper exploration of the…

1South China Agricultural University, China The final, formatted version of the article will be published soon. Notify me Receive an email when it is updated You just subscribed to receive the final version of the article The pituitary gland serves as the central…

KEGG ORTHOLOGY: K17062     ORTHOLOGY: K17062 Help Entry K17062                      KO                                      Symbol bgtB Name arginine/lysine/histidine/glutamine transport system substrate-binding and permease protein Pathway Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing  09131 Membrane transport   02010 ABC transporters    K17062  bgtB; arginine/lysine/histidine/glutamine transport system substrate-binding and permease protein 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   02000 Transporters    K17062  bgtB; arginine/lysine/histidine/glutamine transport…

KEGG ORTHOLOGY: K06665     ORTHOLOGY: K06665 Help Entry K06665                      KO                                      Symbol SSN6, CYC8 Name general transcriptional corepressor CYC8 Pathway map04011   MAPK signaling pathway – yeast Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing  09132 Signal transduction   04011 MAPK signaling pathway – yeast    K06665  SSN6, CYC8; general transcriptional corepressor CYC8 09140 Cellular Processes  09143 Cell growth and death   04111…

How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package. 0 @3e18707b Last seen 10 hours ago India I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for my bacteria using makeOrgPackageFromNCBI command. How can I use…

CircRNAs are widely found in eukaryotes and are a class of abundantly expressed, highly tissue-specific, and stable non-coding RNAs that have an essential role in regulating gene expression12. The abnormal expression of circRNAs has been reported in esophageal squamous cell carcinoma13, breast carcinoma14, gastric cancer15, and hepatocellular carcinoma16, which are…

Background: Revealing the process and mechanism of colorectal cancer will facilitate the discovery of new biomarkers and contribute to the development of targeted drugs. Objective: This study aimed to explore the potentially functional circRNA-miRNA-mRNA network in colorectal cancer (CRC), and further explore its mechanism. Methods: Bioinformatics analysis was used to…

Entry 473325            CDS       T01005                                  Symbol RNASE2 Name (RefSeq) non-secretory ribonuclease precursor   KO K01168   pancreatic ribonuclease [EC:4.6.1.18] Organism ptr  Pan troglodytes (chimpanzee) Brite KEGG Orthology (KO) [BR:ptr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03019 Messenger RNA biogenesis [BR:ptr03019]    473325 (RNASE2)   04131 Membrane trafficking [BR:ptr04131]    473325 (RNASE2)Enzymes [BR:ptr01000] 4. Lyases  4.6  Phosphorus-oxygen lyases   4.6.1  Phosphorus-oxygen lyases (only sub-subclass identified to date)    4.6.1.18  pancreatic ribonuclease     473325 (RNASE2)Messenger…

How to do KEGG pathway analysis when I have a gene with multiple entrez IDs? 0 Hello, I did DESeq2 on my samples and I have a list of DEGs that I would like to do kegg pathway analysis on. For DESeq2 I used biomart and tximport to assign external…

3.1. Atypical Morphology of Protein Bodies in the Endosperm of Seeds from Glutelin Gene-Edited Transgenic Rice ER-derived PB-I vacuoles begin to form in response to the aggregation of β-/γ-zeins (maize) and 10-kDa prolamins (rice) and then expand by co-aggregation of α-/δ-zeins (maize) and 13-/16-kDa prolamins (rice) [3,22,23]. Saito’s group reported…

Entry 415125            CDS       T01007                                  Symbol FGFR2 Name (RefSeq) fibroblast growth factor receptor 2 precursor   KO K05093   fibroblast growth factor receptor 2 [EC:2.7.10.1] Organism cfa  Canis lupus familiaris (dog) Pathway cfa01521   EGFR tyrosine kinase inhibitor resistance cfa04010   MAPK signaling pathway cfa04014   Ras signaling pathway cfa04015   Rap1 signaling pathway cfa04020   Calcium signaling pathway cfa04144   Endocytosis…

Entry 18601618          CDS       T02994                                  Name (RefSeq) alpha-glucan phosphorylase 1   KO K00688   glycogen phosphorylase [EC:2.4.1.1] Organism tcc  Theobroma cacao (cacao) Pathway tcc00500   Starch and sucrose metabolism tcc01100   Metabolic pathways tcc01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism  09101 Carbohydrate metabolism   00500 Starch and sucrose metabolism    18601618Enzymes [BR:tcc01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.1  glycogen phosphorylase     18601618 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

In recent decades, the development of computational and bioinformatics tools and websites for life sciences has increased exponentially. This great development has gone hand in hand with the availability of genome, proteome and macromolecule structure databases, and also of functional experiments, including microarray and RNAseq expression data, RNA-protein interactions, ChIP-seq,…

Entry STH138            CDS       T00196                                  Name (GenBank) putative N-acetyl-mannosamine transferase   KO K05946   N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase [EC:2.4.1.187] Organism sth  Symbiobacterium thermophilum Pathway sth00552   Teichoic acid biosynthesis Brite KEGG Orthology (KO) [BR:sth00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00552 Teichoic acid biosynthesis    STH138 09180 Brite Hierarchies  09181 Protein families: metabolism   01003 Glycosyltransferases [BR:sth01003]    STH138Enzymes [BR:sth01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.187  N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase     STH138Glycosyltransferases [BR:sth01003] Polysaccharide  Bacterial polysaccharide (excluding LPS)   STH138 BRITE hierarchy SSDB…

Shen, C.-H. Molecular diagnosis of infectious diseases in Diagnostic Molecular Biology Ch. 15, 387–411 (Academic Press, C 2019). Katholm, J., Bennedsgaard, T. W., Koskinen, M. T. & Rattenborg, E. Quality of bulk tank milk samples from Danish dairy herds based on real-time polymerase chain reaction identification of mastitis pathogens. J….

How to do simple pathway analysis? 1 I have a set of 100 genes (the AA sequences) from a non-model plant species. Now I want to simply identify which pathways they belong to. I want to generate a typical KEGG style image/map highlighting my genes in the entire pathway. I…

DOI: 10.18129/B9.bioc.KEGGdzPathwaysGEO   KEGG Disease Datasets from GEO Bioconductor version: Release (3.18) This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by…

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

Entry 102247935         CDS       T02920                                  Symbol TRMT44 Name (RefSeq) tRNA methyltransferase 44 homolog (S. cerevisiae)   KO K15447   tRNASer (uridine44-2′-O)-methyltransferase [EC:2.1.1.211] Organism myb  Myotis brandtii (Brandt’s bat) Brite KEGG Orthology (KO) [BR:myb00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03016 Transfer RNA biogenesis [BR:myb03016]    102247935 (TRMT44)Enzymes [BR:myb01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.211  tRNASer (uridine44-2′-O)-methyltransferase     102247935 (TRMT44)Transfer RNA biogenesis [BR:myb03016] Eukaryotic type  tRNA modification…

Entry KR75_11080        CDS       T03531                                  Name (GenBank) xylose isomerase   KO K01805   xylose isomerase [EC:5.3.1.5] Organism kvd  Klebsiella variicola DX120E Pathway kvd00040   Pentose and glucuronate interconversions kvd00051   Fructose and mannose metabolism kvd01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:kvd00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    KR75_11080   00051 Fructose and mannose metabolism    KR75_11080Enzymes [BR:kvd01000] 5. Isomerases  5.3  Intramolecular oxidoreductases   5.3.1  Interconverting aldoses and…

Sampling sites and depths Metagenomes were produced from sediment samples at drilling sites U1545B to U1549B that follow a northwest-to-southeast transect across the northwestern flanking region of Guaymas Basin (Fig. 1A) and include an off-axis hydrothermal system, the Ringvent site (Fig. 1B). The samples were selected to coordinate with depths used for…

Entry 1474              CDS       T01001                                  Symbol CST6, ECTD15 Name (RefSeq) cystatin E/M   KO K13902   cystatin-M Organism hsa  Homo sapiens (human) Disease H00651   Hypohidrotic ectodermal dysplasia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:hsa01002]    1474 (CST6)Peptidases and inhibitors [BR:hsa01002] Peptidase inhibitors  Family I25: cystatin family   1474 (CST6) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

Entry 637               CDS       T01001                                  Symbol BID, FP497 Name (RefSeq) BH3 interacting domain death agonist   KO K04726   BH3 interacting domain death agonist Organism hsa  Homo sapiens (human) Pathway hsa01524   Platinum drug resistance hsa04071   Sphingolipid signaling pathway hsa04115   p53 signaling pathway hsa04210   Apoptosis hsa04215   Apoptosis – multiple species hsa04217   Necroptosis hsa04650   Natural killer cell mediated…

KEGG DRUG: Tolbutamide     DRUG: Tolbutamide Help Entry D00380                      Drug                                    Name Tolbutamide (JP18/USP/INN);Orinase (TN) Formula C12H18N2O3S Exact mass 270.1038 Mol weight 270.3479 Structure Mol fileKCF fileDB search Simcomp Neighbor Class Antidiabetic agent DG01508  Sulfonylurea receptor agonist  DG01734  Sulfonylurea DG02044  Hypoglycemic agent  DG01734  Sulfonylurea Remark Efficacy Antidiabetic, Hypoglycemic, Sulfonylurea receptor agonist   Disease Non-insulin-dependent diabetes mellitus, type II [DS:H00409] Comment Sulfonylurea…

Plasmid construction All the constructs used in this study were generated with standard cloning strategies, including PCR, overlapping PCR, oligo annealing, digestion and ligation. Primers were purchased from Genewiz. The plasmid sequence was verified by Sanger sequencing. The pCAG-spike(D614G)-GFP11-mCherry plasmid was modified from Addgene plasmid 158761. Briefly, GFP11 and mCherry…

Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…

Tarnocai C, Canadell JG, Schuur EA, Kuhry P, Mazhitova G, Zimov S. Soil organic carbon pools in the northern circumpolar permafrost region. Global Biogeochem Cycles. 2009;23:1–11. Article  Google Scholar  Hugelius G, Strauss J, Zubrzycki S, Harden JW, Schuur EA, Ping CL, et al. Estimated stocks of circumpolar permafrost carbon with…

Author Contributions Conceptualization, Y.Y. and Y.G.; Data curation, M.L. and W.Z.; Formal analysis, M.L., W.Z., W.T. and J.L.; Funding acquisition, Y.Y. and Y.G.; Investigation, J.X., Y.Y. and Y.G.; Methodology, M.L., J.L. and Y.Y.; Project administration, Y.Y.; Resources, J.X., Y.Y. and Y.G.; Software, M.L., W.Z. and W.T.; Supervision, J.X., Y.Y. and…

Introduction Lung cancer is one of the most common types of cancer worldwide and the leading cause of cancer death.1 The main category of lung cancer is non-small cell lung cancer, accounting for about 85%, and lung adenocarcinoma, as a kind of non-small cell lung cancer, is the most frequently…

Find equivalent pathways between KEGG, Reactome, and WikiPathways 0 Hi everyone, I have to perform a custom pathway analysis to find the ranking/score of some target pathways. I do have the target pathways from KEGG, however I would like to have the equivalent pathways IDs from Reactome and WikiPathway databases…

Doxo and Abe promote cellular senescence accompanied by an altered profile of senescence-related genes in breast cancer cells Doxo and Abe were used to treat breast cancer cells (human triple-negative breast cancer cell line MDA-MB-231 and human luminal A subtype breast cancer cell line MCF-7) for 24 h, without a robust…

Zain ul Arifeen, M., Ma, Y.-N., Xue, Y.-R. & Liu, C.-H. Deep-sea fungi could be the new arsenal for bioactive molecules. Mar. Drugs 18, 9 (2020). Article  Google Scholar  Martínez-Espinosa, R. M. Microorganisms and their metabolic capabilities in the context of the biogeochemical nitrogen cycle at extreme environments. Int. J….

Entry PM0721            CDS       T00046                                  Symbol ttrA Name (GenBank) TtrA   KO K08357   tetrathionate reductase subunit A Organism pmu  Pasteurella multocida subsp. multocida Pm70 Pathway pmu00920   Sulfur metabolism pmu01100   Metabolic pathways pmu01120   Microbial metabolism in diverse environments pmu02020   Two-component system Brite KEGG Orthology (KO) [BR:pmu00001] 09100 Metabolism  09102 Energy metabolism   00920 Sulfur metabolism    PM0721 (ttrA) 09130 Environmental Information Processing  09132 Signal…

KEGG module and abundance of its KEGG Orthologs for functioning 0 Hi all, I’m trying to interpret KEGG Orholog (KO) abundance data from two different groups. As you know, KEGG module is composed of multiple KOs. Then, if I want to say “this KEGG module functions well and actively”, does…

Genome length and GC content Using a hybrid approach that combines Oxford Nanopore long reads and Illumina short reads data, we assembled a scaffold-level version of Ae. koreicus and Ae. japonicus genomes whose size was assessed as 1.24 and 1.39 gigabase (Gb) pairs, respectively. These dimensions resemble those of other…

Patient demographics Among the children, 102 were diagnosed with ARFID, and 33 were healthy. There were 50 males and 52 females in the ARFID group and 15 males and 18 females in the healthy control group (HC group). There was no significant difference in age (P = 0.352) or sex composition (P = 0.512)….

Seeking Advice on Validating RNA-Seq Data Before Differential Analysis 0 Hello, I recently received the RNA-Seq analysis results for a set of samples from a sequencing company. My plan involves the following steps: Perform differential gene expression analysis to obtain a list of differentially expressed genes. Utilize Gene Ontology analysis…

Clinical characteristics of study participants A total of 121 participants were included in the final analyses and were divided into three groups: healthy (n = 44), acute (n = 41), and remission (n = 39). First, the baseline demographic and clinical characteristics of this study are presented in Table 1. The results showed no statistical differences among…

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic bronchitis disease characterized by persistent airflow limitation, which can be prevented and treated. COPD is the third leading cause of death in the world reported in 2020.1 With the progression of the disease, COPD will lead to respiratory failure, pulmonary…

Entry 106522761         CDS       T06063                                  Symbol pak1 Name (RefSeq) serine/threonine-protein kinase PAK 1   KO K04409   p21-activated kinase 1 [EC:2.7.11.1] Organism alim  Austrofundulus limnaeus (annual killifish) Pathway alim04010   MAPK signaling pathway alim04012   ErbB signaling pathway alim04510   Focal adhesion alim04625   C-type lectin receptor signaling pathway alim04810   Regulation of actin cytoskeleton alim05132   Salmonella infection Brite KEGG Orthology…

Entry SAS2563           CDS       T00183                                  Name (GenBank) putative histidinol dehydrogenase   KO K00013   histidinol dehydrogenase [EC:1.1.1.23] Organism sas  Staphylococcus aureus subsp. aureus MSSA476 (MSSA) Pathway sas00340   Histidine metabolism sas01100   Metabolic pathways sas01110   Biosynthesis of secondary metabolites sas01230   Biosynthesis of amino acids Brite KEGG Orthology (KO) [BR:sas00001] 09100 Metabolism  09105 Amino acid metabolism   00340 Histidine metabolism    SAS2563Enzymes [BR:sas01000] 1. Oxidoreductases  1.1  Acting on…

Entry Mlut_12280        CDS       T00918                                  Name (GenBank) Undecaprenyl pyrophosphate synthetase   KO K00806   undecaprenyl diphosphate synthase [EC:2.5.1.31] Organism mlu  Micrococcus luteus Pathway mlu00550   Peptidoglycan biosynthesis mlu00900   Terpenoid backbone biosynthesis mlu01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:mlu00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00550 Peptidoglycan biosynthesis    Mlut_12280  09109 Metabolism of terpenoids and polyketides   00900 Terpenoid backbone biosynthesis    Mlut_12280 09180 Brite…

Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018). Article  CAS  ADS  PubMed  PubMed Central  Google Scholar  Tamburini, S., Shen, N., Wu, H. C. & Clemente, J. C. The microbiome in early life: implications for health outcomes….

Entry BP3287            CDS       T00139                                  Symbol atpG Name (GenBank) ATP synthase gamma chain   KO K02115   F-type H+-transporting ATPase subunit gamma Organism bpe  Bordetella pertussis Tohama I Pathway bpe00190   Oxidative phosphorylation bpe01100   Metabolic pathways Module bpe_M00157   F-type ATPase, prokaryotes and chloroplasts Brite KEGG Orthology (KO) [BR:bpe00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    BP3287 (atpG) 09180 Brite Hierarchies  09181 Protein…

Entry 706234            CDS       T01028                                  Symbol TRAP1 Name (RefSeq) heat shock protein 75 kDa, mitochondrial   KO K09488   TNF receptor-associated protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05012   Parkinson disease mcc05022   Pathways of neurodegeneration – multiple diseases Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09164 Neurodegenerative disease   05012 Parkinson disease    706234 (TRAP1)   05022 Pathways of neurodegeneration –…

Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….

Entry 103675060         CDS       T03271                                  Symbol APPL1 Name (RefSeq) DCC-interacting protein 13-alpha   KO K08733   DCC-interacting protein 13 alpha Organism umr  Ursus maritimus (polar bear) Pathway umr04211   Longevity regulating pathway umr05200   Pathways in cancer umr05210   Colorectal cancer Brite KEGG Orthology (KO) [BR:umr00001] 09150 Organismal Systems  09149 Aging   04211 Longevity regulating pathway    103675060 (APPL1) 09160 Human Diseases  09161 Cancer: overview   05200 Pathways in…

KEGG COMPOUND: C00052     COMPOUND: C00052 Help Entry C00052                      Compound                                Name UDP-alpha-D-galactose;UDP-D-galactose;UDP-galactose;UDP-D-galactopyranose;UDP-alpha-D-galactopyranose Formula C15H24N2O17P2 Exact mass 566.055 Mol weight 566.3018 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00520   Amino sugar and nucleotide sugar metabolism map00541   O-Antigen nucleotide sugar biosynthesis map01250   Biosynthesis of nucleotide sugars Module M00554   Nucleotide sugar biosynthesis, galactose…

[1] H. L. Sanger, G. Klotz, D. Riesner, H. J. Gross, A. K. Kleinschmidt, Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures, Proc. Natl. Acad. Sci. USA, 73 (1976), 3852–3856. doi.org/10.1073/pnas.73.11.3852 doi: 10.1073/pnas.73.11.3852 …

Objective: Our present study utilized case-control research to explore the relationship between specific circRNAs and pediatric obesity through a literature review and bioinformatics and to predict their possible biological functions, providing ideas for epigenetic mechanism studies of pediatric obesity. Methods: CircRNAs related to pediatric obesity were preliminarily screened by a…

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

A database in the Gene Set Enrichment Analysis (GSEA; www.gsea-msigdb.org/gsea/msigdb/index.jsp) platform10,11 was used to identify 134 GLN metabolism-associated genes. Weighted gene co-expression network analysis (WGCNA) and module screening GLN-associated gene sets were investigated using WGCNA. The results demonstrated that when the weighted value was 24 (Fig. 1A), scale independence was greater…